NAME

Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences.

SYNOPSIS

  $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);

  $sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
  $sim = $sim_pair->hit();   # dto - the hit.

  # some properties for the similarity pair
  $expect = $sim_pair->significance();
  $score = $sim_pair->score();
  $bitscore = $sim_pair->bits();

  # this will not write the description for the sequence (only its name)
  print $sim_pair->query()->gff_string(), "\n";

DESCRIPTION

Lightweight similarity search result as a pair of Similarity features. This class inherits off Bio::SeqFeature::FeaturePair and therefore implements Bio::SeqFeatureI, whereas the two features of the pair are descendants of Bio::SeqFeature::Generic, with better support for representing similarity search results in a cleaner way.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bio.perl.org/MailList.html  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHOR - Hilmar Lapp

Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com

Describe contact details here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $similarityPair = new Bio::SeqFeature::SimilarityPair
                                 (-hit   => $hit,
                                  -query => $query,
                                  -source => 'blastp');
 Function: Initializes a new SimilarityPair object
 Returns : Bio::SeqFeature::SimilarityPair
 Args    : -query => The query in a Feature pair 
           -hit   => (formerly '-subject') the subject/hit in a Feature pair

query

 Title   : query
 Usage   : $query_feature = $obj->query();
           $obj->query($query_feature);
 Function: The query object for this similarity pair
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] Bio::SeqFeature::Similarity

See Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair

subject

 Title   : subject
 Usage   : $sbjct_feature = $obj->subject();
           $obj->subject($sbjct_feature);
 Function: Get/Set Subject for a SimilarityPair 
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] Bio::SeqFeature::Similarity
 Notes   : Deprecated.  Use the method 'hit' instead

hit

 Title   : hit
 Usage   : $sbjct_feature = $obj->hit();
           $obj->hit($sbjct_feature);
 Function: Get/Set Hit for a SimilarityPair 
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] Bio::SeqFeature::Similarity

source_tag

 Title   : source_tag
 Usage   : $source = $obj->source_tag(); # i.e., program
           $obj->source_tag($evalue);
 Function: Gets the source tag (program name typically) for a feature 
 Returns : string
 Args    : [optional] string

significance

 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: 
 Returns : 
 Args    :

score

 Title   : score
 Usage   : $score = $obj->score();
           $obj->score($value);
 Function: 
 Returns : 
 Args    :

bits

 Title   : bits
 Usage   : $bits = $obj->bits();
           $obj->bits($value);
 Function: 
 Returns : 
 Args    :

CPAN RT